PDB Short entry for 1H3E HEADER LIGASE 28-AUG-02 1H3E TITLE TYROSYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH WILD- TITLE 2 TYPE TRNATYR(GUA) AND WITH ATP AND TYROSINOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSYL-TRNA SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TYROSINE--TRNA LIGASE; COMPND 5 EC: 6.1.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: WILD-TYPE TRNATYR(GUA); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 262724; SOURCE 4 STRAIN: HB27; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET29B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 13 ORGANISM_TAXID: 274 KEYWDS LIGASE, CLASS I AMINOACYL-TRNA SYNTHETASE: ATP + L-TYROSINE + KEYWDS 2 TRNA(TYR) -> AMP + PPI + L-TYROSYL-TRNA(TYR) EXPDTA X-RAY DIFFRACTION AUTHOR S.CUSACK,A.YAREMCHUK,I.KRIKLIVYI,M.TUKALO REVDAT 9 30-OCT-19 1H3E 1 LINK REVDAT 8 17-OCT-18 1H3E 1 HETSYN REVDAT 7 19-AUG-15 1H3E 1 SEQRES MODRES HET HETNAM REVDAT 7 2 1 FORMUL LINK HETATM REVDAT 6 05-FEB-14 1H3E 1 SOURCE REMARK VERSN REVDAT 5 06-JUL-11 1H3E 1 VERSN REVDAT 4 24-FEB-09 1H3E 1 VERSN REVDAT 3 24-JUN-03 1H3E 1 COMPND LINK REVDAT 2 05-DEC-02 1H3E 1 HEADER COMPND REMARK DBREF REVDAT 1 27-OCT-02 1H3E 0 JRNL AUTH A.YAREMCHUK,I.KRIKLIVYI,M.TUKALO,S.CUSACK JRNL TITL CLASS I TYROSYL-TRNA SYNTHETASE HAS A CLASS II MODE OR TRNA JRNL TITL 2 RECOGNITION JRNL REF EMBO J. V. 21 3829 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 12110594 JRNL DOI 10.1093/EMBOJ/CDF373 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1216869.710 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 22644 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1149 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2774 REMARK 3 BIN R VALUE (WORKING SET) : 0.3670 REMARK 3 BIN FREE R VALUE : 0.3910 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 155 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.031 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3403 REMARK 3 NUCLEIC ACID ATOMS : 1762 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 115.5 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.06000 REMARK 3 B22 (A**2) : 10.06000 REMARK 3 B33 (A**2) : -20.13000 REMARK 3 B12 (A**2) : 22.22000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.63 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.71 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.260 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.210 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.090 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.350 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.150 ; 4.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 46.84 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BASES OF TRNA NUCLEOTIDES 16,20,474, 74 REMARK 3 OMITTED: NOT VISIBLE IN ELECTRON DENSITY. UNIDENTIFIED MODIFIED REMARK 3 BASES IN THE TRNA(E.G ADE-37 IN CHAIN B) HAVE NOT BEEN MODELED. REMARK 4 REMARK 4 1H3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1290011272. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22669 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 23.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.50900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: T. THERMOPHILUS TYROSYL-TRNA SYNTHETASE PREVIOUSLY REMARK 200 DETERMINED BY SIRAS BY SAME AUTHORS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROP: 5MG/ML TYRRSTT+TRNA(TYR)WITH 5MM REMARK 280 TYROSINOL, 10MM MGCL2, 10MM ATP, 50MM HEPES (PH7.0), 0.8M REMARK 280 AMMONIUM SULPHATE. RESERVOIR: 1.5-1.6M AMMONIUM SULPHATE, 100MM REMARK 280 HEPES (PH7.0)., PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.48367 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 72.96733 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 72.96733 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.48367 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE TETRAMER IS ACTUALLY A DIMER OF CHAIN A, REMARK 300 EACH ASSOCIATED WITH A MOLECULE OF CHAIN B GIVING RISE REMARK 300 TO A TETRAMERIC STATE REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 55830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 194.28750 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 -112.17194 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 109.45100 REMARK 400 REMARK 400 COMPOUND REMARK 400 CATALYTIC ACTIVITY: ATP + L-TYROSINE + TRNA(TYR) = AMP + REMARK 400 DIPHOSPHATE + L-TYROSYL-TRNA(TYR). REMARK 400 ALTHOUGH THIS PROTEIN IS A CLASS I AMINOACYL-TRNA REMARK 400 SYNTHETASE, IT DISPLAYS A CLASS II MODE OF TRNA RECOGNITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 THR A 4 REMARK 465 GLY A 5 REMARK 465 C B 75 REMARK 465 A B 76 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 C B 16 N1 C2 O2 N3 C4 N4 C5 REMARK 470 C B 16 C6 REMARK 470 U B 47D N1 C2 O2 N3 C4 O4 C5 REMARK 470 U B 47D C6 REMARK 470 C B 74 C5' C4' O4' C3' O3' C2' O2' REMARK 470 C B 74 C1' N1 C2 O2 N3 C4 N4 REMARK 470 C B 74 C5 C6 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 G B 1 P G B 1 OP3 -0.089 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 8 -72.03 -43.43 REMARK 500 GLU A 9 -39.89 -37.32 REMARK 500 GLU A 20 -71.26 -60.44 REMARK 500 PRO A 46 63.98 -64.31 REMARK 500 ASP A 50 138.11 67.98 REMARK 500 ARG A 89 137.32 -38.95 REMARK 500 PRO A 120 -31.77 -31.78 REMARK 500 ALA A 164 0.27 -65.20 REMARK 500 PRO A 167 133.09 -38.45 REMARK 500 ARG A 187 53.94 39.65 REMARK 500 ARG A 230 -68.32 -102.76 REMARK 500 ASN A 239 23.09 -152.99 REMARK 500 PRO A 260 -4.01 -55.10 REMARK 500 PRO A 285 -70.83 -60.71 REMARK 500 GLU A 333 23.11 -67.79 REMARK 500 GLU A 334 -34.55 -134.46 REMARK 500 GLU A 352 -71.75 -53.84 REMARK 500 ALA A 361 -38.43 -39.75 REMARK 500 ARG A 368 -161.31 -119.26 REMARK 500 THR A 404 -7.61 -150.28 REMARK 500 PRO A 415 157.61 -46.04 REMARK 500 ASP A 423 55.35 -140.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 300 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 1433 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYE A 1434 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H3F RELATED DB: PDB REMARK 900 TYROSYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH REMARK 900 TYROSINOL DBREF 1H3E A 1 432 UNP P83453 SYY_THETH 1 432 DBREF 1H3E B 1 76 PDB 1H3E 1H3E 1 76 SEQRES 1 A 432 MET ALA GLY THR GLY HIS THR PRO GLU GLU ALA LEU ALA SEQRES 2 A 432 LEU LEU LYS ARG GLY ALA GLU GLU ILE VAL PRO GLU GLU SEQRES 3 A 432 GLU LEU LEU ALA LYS LEU LYS GLU GLY ARG PRO LEU THR SEQRES 4 A 432 VAL LYS LEU GLY ALA ASP PRO THR ARG PRO ASP LEU HIS SEQRES 5 A 432 LEU GLY HIS ALA VAL VAL LEU ARG LYS MET ARG GLN PHE SEQRES 6 A 432 GLN GLU LEU GLY HIS LYS VAL VAL LEU ILE ILE GLY ASP SEQRES 7 A 432 PHE THR GLY MET ILE GLY ASP PRO SER GLY ARG SER LYS SEQRES 8 A 432 THR ARG PRO PRO LEU THR LEU GLU GLU THR ARG GLU ASN SEQRES 9 A 432 ALA LYS THR TYR VAL ALA GLN ALA GLY LYS ILE LEU ARG SEQRES 10 A 432 GLN GLU PRO HIS LEU PHE GLU LEU ARG TYR ASN SER GLU SEQRES 11 A 432 TRP LEU GLU GLY LEU THR PHE LYS GLU VAL VAL ARG LEU SEQRES 12 A 432 THR SER LEU MET THR VAL ALA GLN MET LEU GLU ARG GLU SEQRES 13 A 432 ASP PHE LYS LYS ARG TYR GLU ALA GLY ILE PRO ILE SER SEQRES 14 A 432 LEU HIS GLU LEU LEU TYR PRO PHE ALA GLN ALA TYR ASP SEQRES 15 A 432 SER VAL ALA ILE ARG ALA ASP VAL GLU MET GLY GLY THR SEQRES 16 A 432 ASP GLN ARG PHE ASN LEU LEU VAL GLY ARG GLU VAL GLN SEQRES 17 A 432 ARG ALA TYR GLY GLN SER PRO GLN VAL CYS PHE LEU MET SEQRES 18 A 432 PRO LEU LEU VAL GLY LEU ASP GLY ARG GLU LYS MET SER SEQRES 19 A 432 LYS SER LEU ASP ASN TYR ILE GLY LEU THR GLU PRO PRO SEQRES 20 A 432 GLU ALA MET PHE LYS LYS LEU MET ARG VAL PRO ASP PRO SEQRES 21 A 432 LEU LEU PRO SER TYR PHE ARG LEU LEU THR ASP LEU GLU SEQRES 22 A 432 GLU GLU GLU ILE GLU ALA LEU LEU LYS ALA GLY PRO VAL SEQRES 23 A 432 PRO ALA HIS ARG VAL LEU ALA ARG LEU LEU THR ALA ALA SEQRES 24 A 432 TYR ALA LEU PRO GLN ILE PRO PRO ARG ILE ASP ARG ALA SEQRES 25 A 432 PHE TYR GLU SER LEU GLY TYR ALA TRP GLU ALA PHE GLY SEQRES 26 A 432 ARG ASP LYS GLU ALA GLY PRO GLU GLU VAL ARG ARG ALA SEQRES 27 A 432 GLU ALA ARG TYR ASP GLU VAL ALA LYS GLY GLY ILE PRO SEQRES 28 A 432 GLU GLU ILE PRO GLU VAL THR ILE PRO ALA SER GLU LEU SEQRES 29 A 432 LYS GLU GLY ARG ILE TRP VAL ALA ARG LEU PHE THR LEU SEQRES 30 A 432 ALA GLY LEU THR PRO SER ASN ALA GLU ALA ARG ARG LEU SEQRES 31 A 432 ILE GLN ASN ARG GLY LEU ARG LEU ASP GLY GLU VAL LEU SEQRES 32 A 432 THR ASP PRO MET LEU GLN VAL ASP LEU SER ARG PRO ARG SEQRES 33 A 432 ILE LEU GLN ARG GLY LYS ASP ARG PHE VAL ARG VAL ARG SEQRES 34 A 432 LEU SER ASP SEQRES 1 B 86 G G G C A G G U U C C C G SEQRES 2 B 86 A G C G G C C A A A G G G SEQRES 3 B 86 G A C G G U C U G PSU A A A SEQRES 4 B 86 A C C G U U G G C G U A U SEQRES 5 B 86 G C C U U C G C U G G 5MU PSU SEQRES 6 B 86 C G 1MA A U C C A G C C C U SEQRES 7 B 86 G C C C A C C A MODRES 1H3E PSU B 35 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1H3E 5MU B 54 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 1H3E PSU B 55 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1H3E 1MA B 58 A HET PSU B 35 20 HET 5MU B 54 21 HET PSU B 55 20 HET 1MA B 58 23 HET ATP A1433 31 HET TYE A1434 12 HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM 1MA 6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM TYE 4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PHENOL HETSYN TYE TYROSINOL, BOUND FORM OF TYROSINAL FORMUL 2 PSU 2(C9 H13 N2 O9 P) FORMUL 2 5MU C10 H15 N2 O9 P FORMUL 2 1MA C11 H16 N5 O7 P FORMUL 3 ATP C10 H16 N5 O13 P3 FORMUL 4 TYE C9 H13 N O2 FORMUL 5 HOH *13(H2 O) HELIX 1 1 THR A 7 ARG A 17 1 11 HELIX 2 2 PRO A 24 GLU A 34 1 11 HELIX 3 3 HIS A 52 GLU A 67 1 16 HELIX 4 4 PHE A 79 GLY A 84 1 6 HELIX 5 5 THR A 97 GLY A 113 1 17 HELIX 6 6 ASN A 128 GLU A 133 1 6 HELIX 7 7 THR A 136 THR A 144 1 9 HELIX 8 8 SER A 145 MET A 147 5 3 HELIX 9 9 THR A 148 LEU A 153 1 6 HELIX 10 10 ARG A 155 ALA A 164 1 10 HELIX 11 11 SER A 169 LEU A 173 5 5 HELIX 12 12 LEU A 174 ILE A 186 1 13 HELIX 13 13 GLN A 197 TYR A 211 1 15 HELIX 14 14 PRO A 246 MET A 255 1 10 HELIX 15 15 PRO A 258 PRO A 260 5 3 HELIX 16 16 LEU A 261 THR A 270 1 10 HELIX 17 17 GLU A 273 GLY A 284 1 12 HELIX 18 18 GLY A 284 TYR A 300 1 17 HELIX 19 19 ASP A 310 LEU A 317 1 8 HELIX 20 20 ALA A 320 PHE A 324 5 5 HELIX 21 21 GLU A 334 GLY A 348 1 15 HELIX 22 22 PRO A 360 LEU A 364 5 5 HELIX 23 23 VAL A 371 ALA A 378 1 8 HELIX 24 24 SER A 383 ASN A 393 1 11 SHEET 1 AA 6 GLU A 21 VAL A 23 0 SHEET 2 AA 6 VAL A 217 MET A 221 -1 O CYS A 218 N VAL A 23 SHEET 3 AA 6 VAL A 190 GLY A 194 1 O GLU A 191 N PHE A 219 SHEET 4 AA 6 THR A 39 ALA A 44 1 O THR A 39 N VAL A 190 SHEET 5 AA 6 LYS A 71 ILE A 76 1 O LYS A 71 N VAL A 40 SHEET 6 AA 6 PHE A 123 TYR A 127 1 O GLU A 124 N LEU A 74 SHEET 1 AB 5 GLU A 356 ILE A 359 0 SHEET 2 AB 5 ARG A 424 LEU A 430 1 O ARG A 427 N VAL A 357 SHEET 3 AB 5 ARG A 416 ARG A 420 -1 O ARG A 416 N VAL A 428 SHEET 4 AB 5 LEU A 396 LEU A 398 -1 O ARG A 397 N GLN A 419 SHEET 5 AB 5 GLU A 401 VAL A 402 -1 O GLU A 401 N LEU A 398 SHEET 1 AC 2 ILE A 369 TRP A 370 0 SHEET 2 AC 2 GLN A 409 VAL A 410 -1 O VAL A 410 N ILE A 369 LINK O3' G B 34 P PSU B 35 1555 1555 1.60 LINK O3' PSU B 35 P A B 36 1555 1555 1.61 LINK O3' G B 53 P 5MU B 54 1555 1555 1.61 LINK O3' 5MU B 54 P PSU B 55 1555 1555 1.61 LINK O3' PSU B 55 P C B 56 1555 1555 1.61 LINK O3' G B 57 P 1MA B 58 1555 1555 1.60 LINK O3' 1MA B 58 P A B 59 1555 1555 1.61 CISPEP 1 VAL A 23 PRO A 24 0 -1.25 SITE 1 AC1 19 GLY A 43 ALA A 44 ASP A 45 HIS A 52 SITE 2 AC1 19 GLY A 54 HIS A 55 VAL A 58 ARG A 93 SITE 3 AC1 19 GLY A 193 GLY A 194 GLN A 197 PRO A 222 SITE 4 AC1 19 LEU A 223 LEU A 224 LYS A 232 MET A 233 SITE 5 AC1 19 SER A 234 LYS A 235 TYE A1434 SITE 1 AC2 10 LYS A 41 GLY A 43 ASP A 45 ASP A 85 SITE 2 AC2 10 TYR A 175 GLN A 179 ASP A 182 GLU A 191 SITE 3 AC2 10 GLN A 197 ATP A1433 CRYST1 129.525 129.525 109.451 90.00 90.00 120.00 P 31 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007721 0.004457 0.000000 0.00000 SCALE2 0.000000 0.008915 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009137 0.00000